# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:22:48 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@@H]1[C@H](C)[C@@H](N=C1C(O)=O)[C@H](C=O)[C@@H](C)O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 6B8  6B8  '(2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid'  ligand  34  17  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6B8
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 6B8  OXT  O  OH1   0  -0.576   1.4279   2.8638  -1.0957
 6B8  C05  C  C     0   0.495   1.9496   2.0308  -0.2168
 6B8  O    O  O     0  -0.413   3.0341   2.1511   0.2917
 6B8  C04  C  CR5   0   0.186   1.0354   0.9009   0.1170
 6B8  C09  C  CR15  0  -0.444   1.4933  -0.3923   0.7440
 6B8  S17  S  S2    0   0.003   3.0713  -1.0162   0.1141
 6B8  C18  C  CH3   0  -0.768   3.2835  -2.4129   1.2399
 6B8  C10  C  CR15  0  -0.254   0.2396  -1.2674   0.5215
 6B8  C11  C  CH3   0  -0.684   0.2687  -2.0671  -0.7712
 6B8  C12  C  CR15  0  -0.109  -0.8464  -0.1690   0.5648
 6B8  N1   N  N     0  -0.324  -0.2184   1.0285   0.0170
 6B8  C13  C  CH1   0  -0.422  -2.2082  -0.4467  -0.0790
 6B8  C02  C  C1    0   0.184  -2.1430  -0.4168  -1.5826
 6B8  O01  O  O     0  -0.376  -2.6895  -1.2100  -2.3089
 6B8  C14  C  CH1   0   0.054  -3.2521   0.6063   0.3942
 6B8  O16  O  OH1   0  -0.652  -3.3120   0.6457   1.8019
 6B8  C15  C  CH3   0  -0.699  -4.6317   0.3705  -0.2024
 6B8  H1   H  HOH1  0   0.492   2.0411   3.5960  -1.2626
 6B8  H3   H  HCR5  0   0.323   1.6196  -0.2104   1.8198
 6B8  H4   H  HCH3  0   0.267   3.2874  -2.0775   2.2762
 6B8  H5   H  HCH3  0   0.263   2.5081  -3.1649   1.1041
 6B8  H6   H  HCH3  0   0.281   4.2480  -2.8649   1.0165
 6B8  H7   H  HCR5  0   0.270   0.1053  -1.9534   1.3592
 6B8  H8   H  HCH3  0   0.254   1.1003  -2.7707  -0.7765
 6B8  H9   H  HCH3  0   0.248  -0.6442  -2.6527  -0.8772
 6B8  H10  H  HCH3  0   0.229   0.3817  -1.4374  -1.6559
 6B8  H11  H  HCR5  0   0.291  -1.0430   0.0525   1.6197
 6B8  H14  H  HCH1  0   0.275  -2.5620  -1.4366   0.2313
 6B8  H15  H  H     0   0.202  -1.5769   0.4327  -2.0047
 6B8  H16  H  HCH1  0   0.241  -2.8968   1.5953   0.0913
 6B8  H17  H  HOH1  0   0.448  -3.6987  -0.1806   2.1138
 6B8  H18  H  HCH3  0   0.230  -4.9881  -0.6411   0.0071
 6B8  H19  H  HCH3  0   0.248  -5.3430   1.0773   0.2253
 6B8  H20  H  HCH3  0   0.239  -4.6464   0.5124  -1.2823

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 6B8  O    C05  double  1.204  0.020  1.204
 6B8  OXT  C05  single  1.318  0.020  1.318
 6B8  C05  C04  single  1.491  0.020  1.491
 6B8  C18  S17  single  1.806  0.020  1.806
 6B8  C04  C09  single  1.508  0.020  1.508
 6B8  C04  N1   double  1.264  0.020  1.264
 6B8  S17  C09  single  1.810  0.020  1.810
 6B8  C09  C10  single  1.545  0.020  1.545
 6B8  N1   C12  single  1.459  0.020  1.459
 6B8  C10  C12  single  1.545  0.020  1.545
 6B8  C10  C11  single  1.520  0.020  1.520
 6B8  O01  C02  double  1.206  0.020  1.206
 6B8  C12  C13  single  1.532  0.020  1.532
 6B8  C02  C13  single  1.505  0.020  1.505
 6B8  C13  C14  single  1.556  0.020  1.556
 6B8  C14  O16  single  1.410  0.020  1.410
 6B8  C14  C15  single  1.521  0.020  1.521
 6B8  OXT  H1   single  0.850  0.020  0.980
 6B8  C09  H3   single  0.970  0.020  1.090
 6B8  C18  H4   single  0.970  0.020  1.090
 6B8  C18  H5   single  0.970  0.020  1.090
 6B8  C18  H6   single  0.970  0.020  1.090
 6B8  C10  H7   single  0.970  0.020  1.090
 6B8  C11  H8   single  0.970  0.020  1.090
 6B8  C11  H9   single  0.970  0.020  1.090
 6B8  C11  H10  single  0.970  0.020  1.090
 6B8  C12  H11  single  0.970  0.020  1.090
 6B8  C13  H14  single  0.970  0.020  1.090
 6B8  C02  H15  single  0.930  0.020  1.080
 6B8  C14  H16  single  0.970  0.020  1.090
 6B8  O16  H17  single  0.850  0.020  0.980
 6B8  C15  H18  single  0.970  0.020  1.090
 6B8  C15  H19  single  0.970  0.020  1.090
 6B8  C15  H20  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 6B8  H1   OXT  C05  109.97  3.000
 6B8  C04  C05  O    122.24  3.000
 6B8  C04  C05  OXT  112.66  3.000
 6B8  O    C05  OXT  125.10  3.000
 6B8  N1   C04  C09  114.86  3.000
 6B8  N1   C04  C05  120.92  3.000
 6B8  C09  C04  C05  123.82  3.000
 6B8  H3   C09  C10  109.16  3.000
 6B8  H3   C09  S17  107.32  3.000
 6B8  C10  C09  S17  117.52  3.000
 6B8  H3   C09  C04  107.46  3.000
 6B8  C10  C09  C04  100.33  3.000
 6B8  S17  C09  C04  114.55  3.000
 6B8  C18  S17  C09   98.74  3.000
 6B8  H6   C18  H5   108.58  3.000
 6B8  H6   C18  H4   108.67  3.000
 6B8  H5   C18  H4   109.51  3.000
 6B8  H6   C18  S17  107.29  3.000
 6B8  H5   C18  S17  111.88  3.000
 6B8  H4   C18  S17  110.81  3.000
 6B8  H7   C10  C12  109.82  3.000
 6B8  H7   C10  C11  108.93  3.000
 6B8  C12  C10  C11  114.28  3.000
 6B8  H7   C10  C09  110.21  3.000
 6B8  C11  C10  C09  113.88  3.000
 6B8  C12  C10  C09   99.42  3.000
 6B8  H10  C11  H9   108.53  3.000
 6B8  H10  C11  H8   106.84  3.000
 6B8  H9   C11  H8   106.97  3.000
 6B8  H10  C11  C10  112.81  3.000
 6B8  H9   C11  C10  110.45  3.000
 6B8  H8   C11  C10  111.01  3.000
 6B8  H11  C12  C13  106.37  3.000
 6B8  H11  C12  N1   105.84  3.000
 6B8  C13  C12  N1   111.94  3.000
 6B8  H11  C12  C10  107.26  3.000
 6B8  C13  C12  C10  118.96  3.000
 6B8  N1   C12  C10  105.69  3.000
 6B8  C12  N1   C04  108.32  3.000
 6B8  H14  C13  C14  107.97  3.000
 6B8  H14  C13  C02  108.34  3.000
 6B8  C14  C13  C02  108.62  3.000
 6B8  H14  C13  C12  109.37  3.000
 6B8  C14  C13  C12  110.23  3.000
 6B8  C02  C13  C12  112.20  3.000
 6B8  H15  C02  O01  120.51  3.000
 6B8  H15  C02  C13  114.78  3.000
 6B8  O01  C02  C13  124.66  3.000
 6B8  H16  C14  C15  109.04  3.000
 6B8  H16  C14  O16  105.38  3.000
 6B8  C15  C14  O16  110.94  3.000
 6B8  H16  C14  C13  108.04  3.000
 6B8  C15  C14  C13  112.59  3.000
 6B8  O16  C14  C13  110.55  3.000
 6B8  H17  O16  C14  108.43  3.000
 6B8  H20  C15  H19  107.20  3.000
 6B8  H20  C15  H18  107.83  3.000
 6B8  H19  C15  H18  108.19  3.000
 6B8  H20  C15  C14  112.38  3.000
 6B8  H19  C15  C14  109.71  3.000
 6B8  H18  C15  C14  111.35  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 6B8  CONST_01  H1   OXT  C05  C04  180.00   0.0  0
 6B8  Var_01    C09  C04  C05  OXT  160.89  30.0  2
 6B8  Var_02    H4   C18  S17  C09  -58.11  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 6B8  chir_01  C09  C04  S17  C10  positiv
 6B8  chir_02  C10  C09  C12  C11  negativ
 6B8  chir_03  C12  N1   C10  C13  positiv
 6B8  chir_04  C13  C12  C02  C14  positiv
 6B8  chir_05  C14  O16  C13  C15  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 6B8  plan-1  OXT  0.020
 6B8  plan-1  C05  0.020
 6B8  plan-1  O    0.020
 6B8  plan-1  C04  0.020
 6B8  plan-1  H1   0.020
 6B8  plan-2  C13  0.020
 6B8  plan-2  C02  0.020
 6B8  plan-2  O01  0.020
 6B8  plan-2  H15  0.020

